org.hkijena.jipipe.api.nodes.algorithm

Class JIPipeIteratingAlgorithm

java.lang.Object

org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

org.hkijena.jipipe.api.nodes.JIPipeGraphNode

org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeIteratingAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable

Direct Known Subclasses:

AnalyzeSkeleton2D3DAlgorithm, AnnotateByImageStatisticsExpressionAlgorithm, AnnotateDataWithImagePropertiesAlgorithm, AnnotateDataWithTableValues, AnnotateWithData, AnnotateWithOverlapMeasureLabelsAlgorithm, AutoThreshold2DAlgorithm, AverageKeyValueThresholdStatisticsGenerator, BitwiseLogicalOperationAlgorithm, BlendImagesAlgorithm, ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm, ChangeRoiPropertiesFromExpressionsAlgorithm, ChangeRoiPropertiesFromTableAlgorithm, ClassicWatershedSegmentationAlgorithm, Clij2ExecuteKernelIterating, CLIJCommandNode, Coloc2Node, ColorRoi3DByStatisticsAlgorithm, ColorRoiByStatisticsAlgorithm, ConcatenatePaths, ConnectVerticesAlgorithm, ConnectVerticesFastAlgorithm, ConvertFilamentsToLabels2Algorithm, ConvertFilamentsToLabelsAlgorithm, ConvertFilamentsToMaskAlgorithm, ConvertFilamentsToRGBAlgorithm, ConvolveByImage2DAlgorithm, CopyFilamentsAcrossZCTAlgorithm, CopyPath, CopyPhysicalDimensionsBetweenImagesAlgorithm, CropToRoiAlgorithm, CustomAutoThreshold2D16UAlgorithm, CustomAutoThreshold2D16Uv2Algorithm, CustomAutoThreshold2D32FAlgorithm, CustomAutoThreshold2D32Fv2Algorithm, CustomAutoThreshold2D8UAlgorithm, CustomAutoThreshold2D8Uv2Algorithm, DrawLineOvalRectangleRoiAlgorithm, DrawOvalRoiAlgorithm, DrawRectangleRoiAlgorithm, DrawScaleBarRoiAlgorithm, DrawTextRoiAlgorithm, EnlargeShrinkRoiAlgorithm, ErodedVolumeFraction3DAlgorithm, ExportData, ExportImage2Algorithm, ExportImageAlgorithm, ExportImageDirectorySlotAlgorithm, ExportImpImageAlgorithm, ExportROI3DAlgorithm, ExportROI3DAlgorithm2, ExportROIAlgorithm, ExportROIAlgorithm2, ExportScene3DToColladaAlgorithm, ExportScene3DToColladaAlgorithm2, ExportTableAlgorithm, ExportTableAlgorithm2, ExtractFromROIAlgorithm, ExtractImageInRoiAlgorithm, ExtractLabelStatisticsAlgorithm, ExtractRoi2DRelationStatisticsAlgorithm, ExtractRoi3DRelationStatisticsAlgorithm, ExtractRoi3DStatisticsAlgorithm, ExtractROIProfileAlgorithm, FastImageArithmeticsAlgorithm, FastKeyValueThresholdStatisticsGenerator, FFTCustomFilter, FilterAndMergeRoiByStatisticsScriptAlgorithm, FilterLabelsByMaskAlgorithm, FilterLabelsByOverlapAlgorithm, FilterLabelsByStatisticsAlgorithm, FilterLabelsByThicknessAlgorithm, FilterRoi3DByOverlapAlgorithm, FilterRoi3DByStatisticsAlgorithm, FilterROIByOverlapAlgorithm, FilterRoiByStatisticsAlgorithm, FilterRoiByStatisticsScriptAlgorithm, FixOverlapsNonBranchingAlgorithm, FollowSpotsPerTrackNode, GeodesicDistanceMap2DAlgorithm, GetRoiImageAlgorithm, GrayscaleAttributeFiltering2DAlgorithm, GrayscaleAttributeFiltering3DAlgorithm, ImageCalculator2DExpression, ImageComparer2DAlgorithm, ImageJ2OpNode, ImageStatisticsAlgorithm, ImageStatisticsExpressionAlgorithm, ImageToTableColumnAlgorithm, ImportWekaModelFromFileAlgorithm, ImposeMaxima2DAlgorithm, ImposeMaxima3DAlgorithm, InpaintingAlgorithm, IteratingJythonScriptAlgorithm, IteratingPythonScriptAlgorithm, IteratingRScriptAlgorithm, IterativeThreshold3DAlgorithm, IterativeThresholdByROIStatistics2DAlgorithm, KeyValueAveragesGenerator, KeyValueHistogramGenerator, KeyValueThresholdPartitionAveragesGenerator, KeyValueThresholdPartitionGenerator, KeyValueThresholdStatisticsGenerator, LegacyImageCalculator2DAlgorithm, LineMirror2DFromRoiAlgorithm, LocalImageCalculator2DExpression, MacroWrapperAlgorithm, MergeAnnotations, MergeChannelsAlgorithm, MergeHSBChannelsAlgorithm, MergeImagesAlgorithm, MergeLABChannelsAlgorithm, MergeLabelsAlgorithm, MergeLabelsToBinsAlgorithm, MergeLabelsToThicknessAlgorithm, MergeParametersAlgorithm, MergeRGBChannelsAlgorithm, MergeSmallLabelsAlgorithm, MergeTableColumnsSupplementAlgorithm, MontageToStackAlgorithm, MorphologicalReconstruction2DAlgorithm, MorphologicalReconstruction3DAlgorithm, MultipleImagesToTableAlgorithm, OMEImageFromImagePlus, OverlapMeasureLabelsAlgorithm, OverlayImagesAlgorithm, OverwriteAnnotations, PathsToJIPipeProjectParametersAlgorithm, ReferencedAppendRectangularRoiAlgorithm, ReferencedDefineRectangularRoiAlgorithm, RegisterRoiToImageByBrightnessAlgorithm, RelativizePaths, RemoveBorderFilaments, RemoveBorderRoi3DAlgorithm, RemoveBorderRoisAlgorithm, ReplaceLabelsByTableAlgorithm, Roi3DToLabelsAlgorithm, Roi3DToMaskAlgorithm, Roi3DToRGBAlgorithm, RoiFloodFillAlgorithm, RoiStatisticsAlgorithm, ROIToLabelsByNameAlgorithm, ROIToLabelsExpressionAlgorithm, RoiToMaskAlgorithm, RoiToRGBAlgorithm, RotateRoiAlgorithm, RunProcessIteratingAlgorithm, SeededWatershedSegmentationAlgorithm, SetImageMetadataFromTableAlgorithm, SetImpAlphaChannelAlgorithm, SetLUTFromImageAlgorithm, SetOverlay3DAlgorithm, SetOverlayAlgorithm, SetOverlayFilamentsAlgorithm, SetROI3DMetadataFromTableAlgorithm, SetRoiImageAlgorithm, SetRoiMetadataByStatisticsAlgorithm, SetROIMetadataFromTableAlgorithm, SetVertexMetadataFromImageAlgorithm, SetVertexPhysicalSizeFromImageAlgorithm, SetVertexRadiusFromImageAlgorithm, SetVertexValueFromImageAlgorithm, SimpleImageAndRoiIteratingAlgorithm, SimpleImageRegistrationAlgorithm, SingleIterationStepCheckerAlgorithm, SkeletonToSimplifiedFilamentsFijiAlgorithm, SortAndExtractRoiByStatisticsAlgorithm, SortAndExtractRoiByStatisticsAlgorithm2, SortRoiListByExpressionsAndMeasurementsAlgorithm, SplitChannelsByTableAlgorithm, SplitRoi3DIntoConnectedComponentsAlgorithm, SplitRoiConnectedComponentsAlgorithm, SpotDetectorNode, SpotSegmentation3DAlgorithm, SpotsToRGBNode, StackCombinerAlgorithm, StackToDimensionMerger2Algorithm, StackToMontage2Algorithm, StackToMontageAlgorithm, TrackingNode, TracksToRGBNode, TransformEqualizeDimensionsAlgorithm, TransformExpandCanvas2DAlgorithm, TurboRegRegistration2DReferencedAlgorithm, TurboRegRegistration2DSingleAlgorithm, UploadOMEROImageToDatasetAlgorithm, UploadOMEROTableAlgorithm, Warp2DAlgorithm, Watershed3DSegmentationAlgorithm, Watershed3DSplittingAlgorithm, WekaClassification2DAlgorithm, WekaClassification3DAlgorithm, WekaTrainingLabels2DAlgorithm, WekaTrainingMask2DAlgorithm, WekaTrainingROI2DAlgorithm, WekaTrainingROI3DAlgorithm

public abstract class JIPipeIteratingAlgorithm
extends JIPipeParameterSlotAlgorithm
implements JIPipeParallelizedAlgorithm, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm

An JIPipeAlgorithm that iterates through each data row. This algorithm utilizes the JIPipeSingleIterationStep class to iterate through input data sets. It offers various parameters that control how data sets are matched. If your algorithm only has one input and will never have more than one input slot, we recommend using JIPipeSimpleIteratingAlgorithm instead that comes without the additional data set matching strategies

Nested Class Summary

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.BaseDirectoryChangedEventEmitter, JIPipeGraphNode.BaseDirectoryChangedEventListener, JIPipeGraphNode.NodeSlotsChangedEvent, JIPipeGraphNode.NodeSlotsChangedEventEmitter, JIPipeGraphNode.NodeSlotsChangedEventListener, JIPipeGraphNode.Serializer

Nested classes/interfaces inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterChangedEventEmitter, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEventEmitter, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEvent, JIPipeParameterCollection.ParameterUIChangedEventEmitter, JIPipeParameterCollection.ParameterUIChangedEventListener

Field Summary

Fields inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
JIPipeIteratingAlgorithm(JIPipeIteratingAlgorithm other) Copies the algorithm
JIPipeIteratingAlgorithm(JIPipeNodeInfo info) Creates a new instance
JIPipeIteratingAlgorithm(JIPipeNodeInfo info, JIPipeSlotConfiguration slotConfiguration) Creates a new instance

Method Summary

Modifier and Type	Method and Description
void	createUIInputSlotIconDescriptionMenuItems(String slotName, List<ViewOnlyMenuItem> target) Explanations added to the slot menu Can be null
JIPipeDataBatchGenerationResult	generateDataBatchesGenerationResult(List<JIPipeInputDataSlot> slots, JIPipeProgressInfo progressInfo) Generates iteration steps.
JIPipeAdaptiveParameterSettings	getAdaptiveParameterSettings()
JIPipeIteratingAlgorithmIterationStepGenerationSettings	getDataBatchGenerationSettings()
JIPipeIterationStepGenerationSettings	getGenerationSettingsInterface() Returns the batch generation settings as interface
int	getParallelizationBatchSize() Returns how many threads the actual algorithm requires.
protected boolean	isAllowEmptyIterationStep() If true, allow the execution of an empty iteration step if all inputs are optional and are empty
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Allows to override the visibility of parameters inside the UI
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterCollection subParameter) Allows to override the visibility of sub-parameters inside the UI
protected abstract void	runIteration(JIPipeSingleIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs code on one data row
void	runParameterSet(JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo, List<JIPipeTextAnnotation> parameterAnnotations) Runs a parameter set iteration
protected void	runPassThrough(JIPipeProgressInfo progressInfo, JIPipeSingleIterationStep iterationStep) A pass-through variant for iterating algorithms.
boolean	supportsParallelization() Indicates to the algorithm base implementation if parallelization is supported.

Methods inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, onParameterChanged, run

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, onDeserialized, reportValidity, runPassThrough, setEnabled, setPassThrough, setRuntimePartition, setSkipped

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

archiveTo, canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, emitNodeSlotsChangedEvent, fromJson, getAliasIdInParentGraph, getBaseDirectory, getBaseDirectoryChangedEventEmitter, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getCustomName, getDependencies, getDisplayName, getEnvironmentDependencies, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getName, getNewScratch, getNodeSlotsChangedEventEmitter, getNodeUILocationPerViewModePerCompartment, getNodeUILocationWithin, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProject, getProjectCompartment, getProjectDataDirs, getProjectDirectory, getRuntimeProject, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getTextDescription, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, onSlotConfigurationChanged, renderInputSlots, renderOutputSlots, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setNodeUILocationPerViewModePerCompartment, setNodeUILocationWithin, setNodeUILocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots

Methods inherited from class org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, onParameterStructureChanged, onParameterUIChanged, registerSubParameter, registerSubParameters

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.hkijena.jipipe.api.nodes.iterationstep.JIPipeIterationStepAlgorithm

generateDataBatchesDryRun

Methods inherited from interface org.hkijena.jipipe.api.nodes.JIPipeAdaptiveParametersAlgorithm

installUIOverrideParameterEditor, installUIParameterOptions

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

deserializeFromJsonNode, emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, serializeToJsonFile, serializeToJsonGenerator, serializeToJsonString, setParameter

Methods inherited from interface org.hkijena.jipipe.api.validation.JIPipeValidatable

generateValidityReport

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterUIChangedEventListener

onParameterUIChanged

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterStructureChangedEventListener

onParameterStructureChanged

Constructor Detail

JIPipeIteratingAlgorithm

public JIPipeIteratingAlgorithm(JIPipeNodeInfo info,
                                JIPipeSlotConfiguration slotConfiguration)

Creates a new instance

Parameters:

info - Algorithm info

slotConfiguration - Slot configuration override

JIPipeIteratingAlgorithm

public JIPipeIteratingAlgorithm(JIPipeNodeInfo info)

Creates a new instance

Parameters:

info - Algorithm info

JIPipeIteratingAlgorithm

public JIPipeIteratingAlgorithm(JIPipeIteratingAlgorithm other)

Copies the algorithm

Parameters:

other - The original

Method Detail

getGenerationSettingsInterface

public JIPipeIterationStepGenerationSettings getGenerationSettingsInterface()

Description copied from interface: JIPipeIterationStepAlgorithm

Returns the batch generation settings as interface

Specified by:

getGenerationSettingsInterface in interface JIPipeIterationStepAlgorithm

Returns:

batch generation settings as interface

generateDataBatchesGenerationResult

public JIPipeDataBatchGenerationResult generateDataBatchesGenerationResult(List<JIPipeInputDataSlot> slots,
                                                                           JIPipeProgressInfo progressInfo)

Description copied from interface: JIPipeIterationStepAlgorithm

Generates iteration steps. This is a dry-run function that should never throw errors

Specified by:

generateDataBatchesGenerationResult in interface JIPipeIterationStepAlgorithm

Parameters:

slots - the data slots

progressInfo - the progress

Returns:

the batches

createUIInputSlotIconDescriptionMenuItems

public void createUIInputSlotIconDescriptionMenuItems(String slotName,
                                                      List<ViewOnlyMenuItem> target)

Description copied from class: JIPipeGraphNode

Explanations added to the slot menu Can be null

Overrides:

createUIInputSlotIconDescriptionMenuItems in class JIPipeParameterSlotAlgorithm

Parameters:

slotName - the slot name

target - the list of menu items

runPassThrough

protected void runPassThrough(JIPipeProgressInfo progressInfo,
                              JIPipeSingleIterationStep iterationStep)

A pass-through variant for iterating algorithms. Passes the iteration step to the single output

Parameters:

progressInfo - progress info

iterationStep - the iteration step

isAllowEmptyIterationStep

protected boolean isAllowEmptyIterationStep()

If true, allow the execution of an empty iteration step if all inputs are optional and are empty

Returns:

whether empty iteration steps are allowed

runParameterSet

public void runParameterSet(JIPipeGraphNodeRunContext runContext,
                            JIPipeProgressInfo progressInfo,
                            List<JIPipeTextAnnotation> parameterAnnotations)

Description copied from class: JIPipeParameterSlotAlgorithm

Runs a parameter set iteration

Specified by:

runParameterSet in class JIPipeParameterSlotAlgorithm

Parameters:

runContext - the run context

progressInfo - progress info from the run

parameterAnnotations - parameter annotations

getAdaptiveParameterSettings

public JIPipeAdaptiveParameterSettings getAdaptiveParameterSettings()

Specified by:

getAdaptiveParameterSettings in interface JIPipeAdaptiveParametersAlgorithm

getDataBatchGenerationSettings

public JIPipeIteratingAlgorithmIterationStepGenerationSettings getDataBatchGenerationSettings()

supportsParallelization

public boolean supportsParallelization()

Description copied from interface: JIPipeParallelizedAlgorithm

Indicates to the algorithm base implementation if parallelization is supported. Use this function to indicate to the algorithm to conditionally enable/disable parallelization.

Specified by:

supportsParallelization in interface JIPipeParallelizedAlgorithm

Returns:

If the algorithm supports automated parallelization.

getParallelizationBatchSize

public int getParallelizationBatchSize()

Description copied from interface: JIPipeParallelizedAlgorithm

Returns how many threads the actual algorithm requires. Based on this value, the base algorithm creates batches.

Specified by:

getParallelizationBatchSize in interface JIPipeParallelizedAlgorithm

Returns:

number of threads used by the workload

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterCollection subParameter)

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of sub-parameters inside the UI

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeParameterSlotAlgorithm

Parameters:

tree - the parameter tree that is used to access this parameter

subParameter - a sub parameter

Returns:

if the parameter is visible inside the UI

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterAccess access)

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of parameters inside the UI

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeAlgorithm

Parameters:

tree - the parameter tree that is used to access this parameter

access - the parameter

Returns:

if the parameter is visible inside the UI

runIteration

protected abstract void runIteration(JIPipeSingleIterationStep iterationStep,
                                     JIPipeIterationContext iterationContext,
                                     JIPipeGraphNodeRunContext runContext,
                                     JIPipeProgressInfo progressInfo)

Runs code on one data row

Parameters:

iterationStep - The data interface

iterationContext - The iteration context

runContext - the run context

progressInfo - the progress info from the run